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  • 1
    Electronic Resource
    Electronic Resource
    Molecular Modeling of the Domain Shared Between CED-4 and its Mammalian Homologue Apaf-1: A Structural Relationship to the G-proteins (1998)
    Springer
    Journal of molecular modeling 4 (1998), S. 83-93 
    Details
    ISSN: 0948-5023
    Keywords: Keywords  Structure prediction ; Apoptosis ; Proto-oncogene proteins ; G-proteins ; Caspase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract   Apoptosis (programmed cell death, PCD) is a characteristic type of cell death in which a regulated cellular response pathway mediated by cysteine proteases of the caspase family and Bcl-2 family proteins results in ordered and non-inflammatory involution of the cell. The CED-4 protein and its recently identified mammalian homologue Apaf-1 are critical but functionally uncharacterized components of the cell death machinery. We present here a three-dimensional molecular model for the central domain of CED-4, its alternatively spliced transcript (CED-4l) and Apaf-1. A novel protein family is identified and structure prediction for the family identifies a G-protein-like fold with high reliability. The three-dimensional model provides a potential structural explanation for the alternatively spliced variant as well as the known point mutations in CED-4. Regions of the CED-4 and Apaf-1 sequences which may interact with caspases and the Bcl-2 family are proposed. This new information provides a structural molecular framework for the interaction of CED-4-like proteins with the caspases and the Bcl-2 family in the regulation of apoptosis which is analogous to G-protein mediated interactions in well-defined signal transduction pathways.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s008940050134
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  • 2
    Electronic Resource
    Electronic Resource
    Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy (1994)
    [s.l.] : Nature Publishing Group
    Nature structural biology 1 (1994), S. 259-263 
    Details
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The fundamental event in biological assembly is association of two biological macromolecules. Here we present a successful, accurate ab initio prediction of the binding of uncomplexed lysozyme to the HyHel5 antibody. The prediction combines pseudo Brownian Monte Carlo minimization with a ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nsb0494-259
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  • 3
    Electronic Resource
    Electronic Resource
    TSG101 may be the prototype of a class of dominant negative ubiquitin regulators (1997)
    [s.l.] : Nature Publishing Group
    Nature genetics 16 (1997), S. 330-331 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The TSG101 gene has been implicated in sporadic breast cancer1. Knockout of the murine orthologue resulted in fibro-blast transformation and ability to form tumours2. The TSG101 protein contains a proline-rich region and a predicted coiled-coil domain, but no functional clues have been extracted ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng0897-330
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  • 4
    Electronic Resource
    Electronic Resource
    Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR (2000)
    Springer
    Journal of computer aided molecular design 14 (2000), S. 593-610 
    Details
    ISSN: 1573-4951
    Keywords: binding free energy ; molecular docking ; RNA structure ; scintillation proximity assay ; structure-based ligand design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docking procedure: rigid docking first, followed by three steps of flexible docking using a pseudobrownian Monte Carlo minimization in torsion angle space with progressively more detailed conformational sampling on a progressively smaller list of top-ranking compounds. To validate the procedure, we successfully docked ligands for five RNA complexes of known structure. For ranking ligands according to binding avidity, an empirical binding free energy function was developed which accounts, in particular, for solvation, isomerization free energy, and changes in conformational entropy. System-specific parameters for the function were derived on a training set of RNA/ligand complexes with known structure and affinity. To validate the free energy function, we screened the entire ACD for ligands for an RNA aptamer which binds l-arginine tightly. The native ligand ranked 17 out of ca. 153,000 compounds screened, i.e., the procedure is able to filter out 〉99.98% of the database and still retain the native ligand. Screening of the ACD for TAR ligands yielded a high rank for all known TAR ligands contained in the ACD and suggested several other potential TAR ligands. Eight of the highest ranking compounds not previously known to be ligands were assayed for inhibition of the Tat-TAR interaction, and two exhibited a CD50 of ca. 1 μM.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008121029716
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  • 5
    Electronic Resource
    Electronic Resource
    ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 488-506 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150503
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  • 6
    Electronic Resource
    Electronic Resource
    Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1105-1112 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151006
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  • 7
    Electronic Resource
    Electronic Resource
    Recognition of distantly related proteins through energy calculations (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 132-140 
    Details
    ISSN: 0887-3585
    Keywords: distant protein folds ; sequence homology ; database searching ; profile analysis ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190206
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  • 8
    Electronic Resource
    Electronic Resource
    A new method for modeling large-scale rearrangements of protein domains (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 410-424 
    Details
    ISSN: 0887-3585
    Keywords: domain movements ; inter-domain linkers ; conformational calculations ; Monte Carlo-minimization method ; Bence-Jones protein ; lysine/arginine/ornithine-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for modeling large-scale rearrangements of protein domains connected by a single- or a double-stranded linker is proposed. Multidomain proteins may undergo substantial domain displacements, while their intradomain structure remains essentially unchanged. The method allows automatic identification of an interdomain linker and builds an all-atom model of a protein structure in internal coordinates. Torsion angles belonging to the interdomain linkers and side chains potentially able to form domain interfaces are set free while all remaining torsions, bond lengths, and bond angles are fixed. Large-scale sampling of the reduced torsion conformational subspace is effected with the “biased probability Monte Carlo-minimization” method [Abagyan, R.A., Totrov, M.M. (1994): J. Mol. Biol. 235, 983-1002]. Solvation and side-chain entropic contributions are added to the energy function. A special procedure has been developed to generate concerted deformations of a double-stranded interdomain linker in such a way that the polypeptide chain continuity is preserved. The method was tested on Bence-Jones protein with a single-stranded linker and lysine/arginine/ornithine-binding (LAO) protein with a double-stranded linker. For each protein, structurally diverse low-energy conformations with ideal covalent geometry were generated, and an overlap between two sets of conformations generated starting from the crystallographically determined “closed” and “open” forms was found. One of the low-energy conformations generated in a run starting from the LAO “closed” form was only 2.2 Å away from the structure of the “open” form. The method can be useful in predicting the scope of possible domain rearrangements of a multidomain protein. Proteins 27:410-424, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Flexible protein-ligand docking by global energy optimization in internal coordinates (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 215-220 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; ligand binding ; flexible docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight protein-ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side-chain entropy in the internal coordinate space of the flexible ligand and the receptor side chains [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. J. Comp. Chem. 15:488-506, 1994] and a Biased-Probability multitorsion move [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994], each accompanied by full local energy minimization. The best docking solutions were further ranked according to the interaction energy, which included intramolecular deformation energies of both receptor and ligand, the interaction energy, surface tension, side-chain entropic contribution, and an electrostatic term evaluated as a boundary element solution of the Poisson equation with the molecular surface as a dielectric boundary. The geometrical accuracy of the docking solutions ranged from 30% to 70% according to the relative displacement error measure at a 1.5 Å scale. Similar results were obtained when the explicit receptor atoms were replaced with a grid potential. Proteins, Suppl. 1:215-220, 1997. © 1998 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 29-37 
    Details
    ISSN: 0887-3585
    Keywords: deformation zones ; prediction map building ; homology modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Five models by homology containing insertions and deletions and ranging from 33% to 48% sequence identity to the known homologue, and one high sequence identity (85%) model were built for the CASP2 meeting. For all five low identity targets: (i) our starting models were improved by the Internal Coordinate Mechanics (ICM) energy optimization, (ii) the refined models were consistently better than those built with the automatic SWISS-MODEL program, and (iii) the refined models differed by less than 2% from the best model submitted, as judged by the residue contact area difference (CAD) measure [Abagyan, R.A., Totrov, M.J. Mol. Biol. 268:678-685, 1997]. The CAD measure is proposed for ranking models built by homology instead of global root-mean-square deviation, which is frequently dominated by insignificant yet large contributions from incorrectly predicted fragments or side chains. We demonstrate that the precise identification of regions of local backbone deviation is an independent and crucial step in the homology modeling procedure after alignment, since aligned fragments can strongly deviate from the template at various distances from the alignment gap or even in the ungapped parts of the alignment. We show that a local alignment score can be used as an indicator of such local deviation. While four short loops of the meeting targets were predicted by database search, the best loop 1 from target T0028, for which the correct database fragment was not found, was predicted by Internal Coordinate Mechanics global energy optimization at 1.2 Å accuracy. A classification scheme for errors in homology modeling is proposed. Proteins, Suppl. 1:29-37, 1997.© 1998 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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